SY-20 = Soft Tissue and Bone Pathology: Diagnostic molecular pathology of bone and soft tissue tumors: techniques, translation and targets – Genomic insights in sarcomas

31st ECP; Nice, FranceTuesday 10 September 2019; 14:45 – Athena AuditoriumAlexander Lazar MD/PhDProfessorDepartments of Pathology, Genomic Medicine & DermatologySarcoma Research Center

DISCLOSURE OF RELATIONSHIPS WITH INDUSTRY

Alexander Lazar MD/PhDTuesday 10 September 2019

31st ECP: Nice, France

SY-20 = Soft Tissue and Bone Pathology: Diagnostic molecular pathology of bone and soft tissue tumors: techniques, translation and

targets – Genomic insights in sarcomas

I have the following financial relationships to disclose:

GSK, Novartis, BMS, Pfizer, Loxo / Bayer, AbbVie, Astra-Zeneca / MedImmune, Merck, Roche / Genentech / Ignyta, ArcherDx, Illumina, ThermoFisher, Beta-Cat

Pharmaceuticals / Iterion Therapeutics, Foghorn Therapeutics, Flagship Pioneering, Human Longevity Inc, Nucleai, Elsevier, SpringerNature, USCAP, CAP, AACR, ASCO,

WHO / IARC, various VC, strategic consultancies, & marketing concerns.

(mostly scientific advisory boards, clinical trials, research / travel support and business / financial strategy consulting)

These relationships are NOT relevant to the educational content of this lecture.

Road Map of the Talk

• Quick sarcoma introduction

• Sarcoma and Cancer Genome introduction

• The Cancer Genome Atlas (TCGA) in a nutshell:

– Sarcoma Biomarker

– Clinical implications of Sarcoma TCGA

– Related sarcoma studies

Sarcoma Classification

• Can be challenging

• Heterogeneous group of tumors with >50

histological subtypes, each with varying clinical

phenotypes and behavior

• Some tumors are unclassifiable

• Many benign entities (100:1), some of which can be

confused for sarcomas

Sarcoma Classification:Histogenesis/Line of Differentiation

Osteosarcoma

Chondrosarcoma

Angiosarcoma

UPS

Liposarcoma

Leiomyosarcoma

Rhabdomyosarcoma

MPNST

Synovial Sarcoma - ?? Ewing Sarcoma/PNET - ??

Courtesy of Dr. Brian Rubin, CCF

ASPS - ??

• Morphologically or by immunohistochemical studies

• Beware of mimics

• Some tumors lack a normal counterpart (i.e. synovial sarcoma)

• Not all tumors with similar differentiation will behave the same

Sarcoma Classification: Line of Differentiation

A-RMS

PLPS

Myogenin

ALT

FNCLCC Grading

• All three numbers are summated to determine degree of differentiation

Grade 1 : 2-3

Grade 2 : 4-5

Grade 3 : 6-8

• Proven to correlated well with survival

• Mitotic Count. In the most mitotically active area, ten successive high-power fields (at 400x magnification=0.1734 mm2) using a 40x objective.

1 0-9 mitoses per 10 HPFs2 10-19 mitoses per 10 HPFs3 >20 mitoses per 10 HPFs

• Tumor necrosis. Evaluated on gross examination and validated with histological sections

0 No tumor necrosis1 <50% tumor necrosis2 >50% tumor necrosis

• Degree of Differentiation. 1-3

Co

ind

re e

t a

l. C

an

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r. 2

00

1; 9

1(1

0):

19

14

-26

.

FNCLCC Grading

Sarcoma Genomic Classification

• Simple karyotype (recurrent)

– Translocation (SS, RMS, DFSP, MLPS, etc)

– Activating Gene Mutations (GIST, desmoid)

• Intermediate (recurrent)

– WD/DD liposarcoma

• Complex karyotype

– TP53, disrupted chromosome management

– UPS, MFS, pleomorphic liposarcoma

Nature. 2013;499(7457):214-8

*

Science. 2013;399(6127):-1546-58

*

Nature. 2013;499(7457):214-8

Nature. 2013;499(7457):214-8

Science. 2013;399(6127):-1546-58

Science. 2013;399(6127):-1546-58

Science. 2013;399(6127):-1546-58

19

TCGA – Integrative Analysis

Modified from The Cancer Genome Atlas Pan-Cancer analysis project

20

Pan-Cancer 33 Effort

22

TCGA Sarcoma Case Selection

23

Tumor Map – Josh Stuart, UCSC

24

Tumor Map

25

Unbalanced Copy Number

26

Unbalanced copy alterations vs somatic mutations

27

COSMIC Mutational Signatures in Sarcoma

28

Mutations in Sarcoma

29

Specific Mutations in SMGs

30

Sarcoma SMGs are tumor suppressors

31

Sarcomas have low and high CNV states

32

Image Analysis & Mutational Signatures

34

Immune Microenvironment

35

Immune Microenvironment

36

UPS: pre-tx and at 20 weeks

Radiology courtesy of Scott Schuetze MD/PhD

37

Leiomyosarcoma

38

Leiomyosarcoma

39

Leiomyosarcoma

40

Leiomyosarcoma

41

Leiomyosarcoma -RPPA

PTEN Loss Correlates with AKT Activation

BRAF NRAS WTn=39 n=18 n=37

-2.6 2.1

Ph

osp

ho

-AK

T Th

r30

8

PTEN

Tumors (n=96)

BR

AF

Mu

tati

on

+ P

TEN

Lo

ss

PT

EN L

oss

• RPPA of 96 OCT-embedded melanoma metastases & 58 cell lines

– Y-axis, P-AKT expression; Color ~ PTEN expression

• Compared PI3K-AKT pathway activation to mutation status

Davies, CCR, 2009

AKT

PI3K

PTEN

NRAS

• Loss of PTEN associated with greater activation of PI3K pathway (P-AKT) than NRAS mutations

• ~Results in tumors and cell lines

Supports that PTEN is the critical regulator pathway in melanoma

Clonal

Tumor

Tumor

Absent Markedly Reduced

Mildly Reduced Normal/Increased

PTEN IHC on FFPE Melanoma

Intensity relative to internal (+)ive controls

Correlation of PTEN loss in melanoma cells with an immune resistance phenotype.

Weiyi Peng et al. Cancer Discov 2016;6:202-216

©2016 by American Association for Cancer Research

Anders

on N

D,

et al. S

cie

nce,

2018.

Anderson ND, et al. Science, 2018.

Pihan GA, Frontiers in Oncol, 2013.

de Pagter M.S., Kloosterman W.P. (2015) The Diverse Effects of Complex Chromosome

Rearrangements and Chromothripsis in Cancer Development. In: Ghadimi B., Ried T. (eds)

Chromosomal Instability in Cancer Cells. Recent Results in Cancer Research, vol 200.

Springer, Chamhttp://neuropathologyblog.blogspot.com/2015/10/chromothripsis.html

A very different picture than in BAF loss-of-function cancer types – this is why

these diseases are different! Different BAF complex mechanisms on

chromatin!

McBride, Pulice et al., Cancer Cell June 2018

RNAseq reveals distinct SS gene expression signature, consistent with different

chromatin changes between SS18-SSX complexes and LOF (i.e. loss of

SMARCB1/loss of SMARCA4 , etc) BAF complexes

Conclusions

• Sarcoma genomics is a bit complicated

• Complex karyotype sarcomas are driven by copy number alterations and loss of TSG

• Translocation-associated sarcomas can have complex mechanisms to produce fusions

• Epigenetics is an important component of sarcoma tumor biology

MDACC & PICI confidential - not for

distribution

Thanks!